[R-sig-phylo] how to modify tip label of a phylogenetic tree

Hello I have downloaded a phylogenetic tree of global birds. (.nex file) Some of its tips are labelled as codes, such as BB3 and BB4. I want to rename the codes with normal family names. Please kindly advise the package and command to do it. Thank you. Elaine [[alternative HTML version

Re: [R-sig-phylo] how to modify tip label of a phylogenetic tree

Elaine, you can read the tree using the 'ape' package in R: library(ape) tree-read.nexus('path_to_your_tree.nex') then, you will find the tip labels in the following vector: tree$tip.label you can change the names by selecting one element in the vector and modifying it, for example:

[R-sig-phylo] transform nexus SETS block into treefinder partition

Hi all, PartitionFinder selected a complex partitioning scheme that I would like to put into a TreeFinder analysis. As far as I know, TreeFinder ignores NEXUS SETS blocks, and so I would have to input the partitioning by hand. I do this normally for repetitive partitions, e.g. codon positions,